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- PDB-4bop: Structure of OTUD1 OTU domain -

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Basic information

Entry
Database: PDB / ID: 4bop
TitleStructure of OTUD1 OTU domain
ComponentsOTU DOMAIN-CONTAINING PROTEIN 1
KeywordsHYDROLASE
Function / homology
Function and homology information


protein K63-linked deubiquitination / protein deubiquitination / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity
Similarity search - Function
Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / OTU domain-containing protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. ...Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. / Freund, S.M.V. / Ovaa, H. / Komander, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis.
Authors: Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. / Freund, S.M.V. / Ovaa, H. / Komander, D.
History
DepositionMay 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OTU DOMAIN-CONTAINING PROTEIN 1
B: OTU DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7234
Polymers34,5332
Non-polymers1902
Water2,648147
1
A: OTU DOMAIN-CONTAINING PROTEIN 1
B: OTU DOMAIN-CONTAINING PROTEIN 1
hetero molecules

A: OTU DOMAIN-CONTAINING PROTEIN 1
B: OTU DOMAIN-CONTAINING PROTEIN 1
hetero molecules

A: OTU DOMAIN-CONTAINING PROTEIN 1
B: OTU DOMAIN-CONTAINING PROTEIN 1
hetero molecules

A: OTU DOMAIN-CONTAINING PROTEIN 1
B: OTU DOMAIN-CONTAINING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,89116
Polymers138,1318
Non-polymers7608
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area25280 Å2
ΔGint-163.3 kcal/mol
Surface area43330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.240, 82.240, 103.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2071-

HOH

21A-2078-

HOH

31B-2064-

HOH

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Components

#1: Protein OTU DOMAIN-CONTAINING PROTEIN 1 / DUBA-7 / OTUD1


Mass: 17266.402 Da / Num. of mol.: 2 / Fragment: RESIDUES 287-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: Q5VV17, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.66 % / Description: NONE
Crystal growDetails: 10% PEG 4K, 20% GLYCEROL, 0.09M NPS

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→51.97 Å / Num. obs: 20153 / % possible obs: 96.8 % / Observed criterion σ(I): 2.3 / Redundancy: 3.2 % / Biso Wilson estimate: 25.64 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.672 Å / SU ML: 0.45 / σ(F): 1.36 / Phase error: 19.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 1029 5.1 %
Rwork0.1616 --
obs0.1636 20143 99.7 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.304 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7133 Å20 Å20 Å2
2--1.7133 Å20 Å2
3----3.4267 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 10 147 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072493
X-RAY DIFFRACTIONf_angle_d1.0173394
X-RAY DIFFRACTIONf_dihedral_angle_d15.298892
X-RAY DIFFRACTIONf_chiral_restr0.071361
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.21090.24131440.21382733X-RAY DIFFRACTION100
2.2109-2.34930.23831410.18852727X-RAY DIFFRACTION100
2.3493-2.53070.23361600.16882709X-RAY DIFFRACTION100
2.5307-2.78530.19971570.16142730X-RAY DIFFRACTION100
2.7853-3.18810.23711450.14122730X-RAY DIFFRACTION100
3.1881-4.01570.16121430.12972741X-RAY DIFFRACTION100
4.0157-34.67690.18631390.17672744X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5653-0.190.23841.0299-0.32241.01730.00530.06360.1418-0.01720.0779-0.0804-0.31560.1032-0.06220.1642-0.04350.04810.13130.00130.147612.60718.071350.8482
21.06990.04620.56510.84360.11930.9571-0.01230.04590.09890.06120.0439-0.0931-0.10980.2083-0.05270.1374-0.0273-0.01760.1374-0.03840.133514.905316.20875.105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2CHAIN B

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